ENST00000557721.2:n.107+19483G>A

Variant names:

• chr14-44577426-C-T
• rs113317269
• ENST00000557721.2:n.107+19483G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000557721.2(LINC02277):​n.107+19483G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0397 in 152,246 control chromosomes in the GnomAD database, including 170 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.040 (170 hom., cov: 33)
• Consequence: LINC02277 ENST00000557721.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738
• Publications: 1 publications found

Genes affected

LINC02277 (HGNC:53193): (long intergenic non-protein coding RNA 2277)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02277	ENST00000557721.2	n.107+19483G>A		intron_variant	Intron 1 of 3	2
LINC02277	ENST00000795526.1	n.107+19483G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0397 AC: 6038 AN: 152128 Hom.: 170 Cov.: 33

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0334

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.0335

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0397 AC: 6048 AN: 152246 Hom.: 170 Cov.: 33 AF XY: 0.0394 AC XY: 2930 AN XY: 74438

African (AFR) AF: 0.0679 AC: 2819 AN: 41538

American (AMR) AF: 0.0260 AC: 398 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3466

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5192

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4820

European-Finnish (FIN) AF: 0.0334 AC: 354 AN: 10598

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0300 AC: 2039 AN: 68018

Other (OTH) AF: 0.0332 AC: 70 AN: 2110

Alfa AF: 0.0338 Hom.: 39

Bravo AF: 0.0395

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.053
DANN	Benign	0.46
PhyloP100		-0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs113317269; hg19: chr14-45046629;